+Open data
-Basic information
Entry | Database: PDB / ID: 2p2x | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | Probable diphthine synthase | ||||||
Keywords | TRANSFERASE / Pyrococcus horikoshii OT3 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Sugahara, M. / Ono, N. / Taketa, M. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Sugahara, M. / Ono, N. / Taketa, M. / Matsuura, Y. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p2x.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p2x.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p2x_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2p2x_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2p2x_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2p2x_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/2p2x ftp://data.pdbj.org/pub/pdb/validation_reports/p2/2p2x | HTTPS FTP |
-Related structure data
Related structure data | 2e8hC 2hr8C 2huqC 2hutC 2huvC 2huxC 2owfC 2owgC 2owkC 2owuC 2owvC 2p5cC 2p5fC 2p6dC 2p6iC 2p6kC 2p6lC 2p9dC 2pb4C 2pb5C 2pb6C 2pcaC 2pcgC 2pchC 2pciC 2pckC 2pcmC 1wngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 29581.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58456, diphthine synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.06 % |
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Crystal grow | Temperature: 295 K / Method: oil microbatch / pH: 5.5 Details: 3.86M Sodium formate, 0.1M Acetate, pH 5.5, oil microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 17870 / Num. obs: 17870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.064 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 8.6 / Num. unique all: 1750 / Rsym value: 0.27 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1WNG Resolution: 2.9→19.75 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.033
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